The impact of sampling, PCR, and sequencing replication on discerning changes in drinking water bacterial community over diurnal time-scales

Bautista-de los Santos, Q., Schroeder, J. L., Blakemore, O., Moses, J., Haffey, M., Sloan, W. and Pinto, A. J. (2016) The impact of sampling, PCR, and sequencing replication on discerning changes in drinking water bacterial community over diurnal time-scales. Water Research, 90, pp. 216-224. (doi:10.1016/j.watres.2015.12.010)

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Abstract

High-throughput and deep DNA sequencing, particularly amplicon sequencing, is being increasingly utilized to reveal spatial and temporal dynamics of bacterial communities in drinking water systems. Whilst the sampling and methodological biases associated with PCR and sequencing have been studied in other environments, they have not been quantified for drinking water. These biases are likely to have the greatest effect on the ability to characterize subtle spatio-temporal patterns influenced by process/environmental conditions. In such cases, intra-sample variability may swamp any underlying small, systematic variation. To evaluate this, we undertook a study with replication at multiple levels including sampling sites, sample collection, PCR amplification, and high throughput sequencing of 16S rRNA amplicons. The variability inherent to the PCR amplification and sequencing steps is significant enough to mask differences between bacterial communities from replicate samples. This was largely driven by greater variability in detection of rare bacteria (relative abundance <0.01%) across PCR/sequencing replicates as compared to replicate samples. Despite this, we captured significant changes in bacterial community over diurnal time-scales and find that the extent and pattern of diurnal changes is specific to each sampling location. Further, we find diurnal changes in bacterial community arise due to differences in the presence/absence of the low abundance bacteria and changes in the relative abundance of dominant bacteria. Finally, we show that bacterial community composition is significantly different across sampling sites for time-periods during which there are typically rapid changes in water use. This suggests hydraulic changes (driven by changes in water demand) contribute to shaping the bacterial community in bulk drinking water over diurnal time-scales.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Pinto, Dr Ameet and Schroeder, Dr Joanna and Sloan, Professor William
Authors: Bautista-de los Santos, Q., Schroeder, J. L., Blakemore, O., Moses, J., Haffey, M., Sloan, W., and Pinto, A. J.
College/School:College of Arts > School of Humanities > Glasgow University Archaeological Research Division
Journal Name:Water Research
Publisher:Elsevier Ltd.
ISSN:0043-1354
ISSN (Online):1879-2448

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
621651Developing an Event Prediction and Correction Framework for Microbial Management in Drinking Water Systems.Ameet PintoEngineering & Physical Sciences Research Council (EPSRC)EP/K035886/1ENG - ENGINEERING INFRASTRUCTURE & ENVIR